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Martins FMS, Godinho R, Palma L. Cores, edges and beyond: insights into the phylogeography of frigatebirds with a focus on ultraperipheral and endemic populations. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01466-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Samayoa AP, Struthers CD, Trnski T, Roberts CD, Liggins L. Molecular phylogenetics reveals the evolutionary history of marine fishes (Actinopterygii) endemic to the subtropical islands of the Southwest Pacific. Mol Phylogenet Evol 2022; 176:107584. [PMID: 35843570 DOI: 10.1016/j.ympev.2022.107584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
Abstract
Remote oceanic islands of the Pacific host elevated levels of actinopterygian (ray-finned fishes) endemism. Characterizing the evolutionary histories of these endemics has provided insight into the generation and maintenance of marine biodiversity in many regions. The subtropical islands of Lord Howe, Norfolk, and Rangitāhua (Kermadec) in the Southwest Pacific are yet to be comprehensively studied. Here, we characterize the spatio-temporal diversification of marine fishes endemic to these Southwest Pacific islands by combining molecular phylogenies and the geographic distribution of species. We built Bayesian ultrametric trees based on open-access and newly generated sequences for five mitochondrial and ten nuclear loci, and using fossil data for time calibration. We present the most comprehensive phylogenies to date for marine ray-finned fish genera, comprising 34 species endemic to the islands, including the first phylogenetic placements for 11 endemics. Overall, our topologies confirm the species status of all endemics, including three undescribed taxa. Our phylogenies highlight the predominant affinity of these endemics with the Australian fish fauna (53%), followed by the East Pacific (15%), and individual cases where the closest sister taxon of our endemic is found in the Northwest Pacific and wider Indo-Pacific. Nonetheless, for a quarter of our focal endemics, their geographic affinity remains unresolved due to sampling gaps within their genera. Our divergence time estimates reveal that the majority of endemic lineages (67.6%) diverged after the emergence of Lord Howe (6.92 Ma), the oldest subtropical island in the Southwest Pacific, suggesting that these islands have promoted diversification. However, divergence ages of some endemics pre-date the emergence of the islands, suggesting they may have originated outside of these islands, or, in some cases, ages may be overestimated due to unsampled taxa. To fully understand the role of the Southwest Pacific subtropical islands as a 'cradle' for diversification, our study advocates for further regional surveys focused on tissue collection for DNA analysis.
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Affiliation(s)
- André P Samayoa
- School of Natural Sciences, Massey University, Auckland 0745, New Zealand.
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
| | - Thomas Trnski
- Natural Sciences, Auckland Museum Tāmaki Paenga Hira, Auckland 1010, New Zealand.
| | - Clive D Roberts
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland 0745, New Zealand; Natural Sciences, Auckland Museum Tāmaki Paenga Hira, Auckland 1010, New Zealand.
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3
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Delrieu-Trottin E, Hartmann-Salvo H, Saenz-Agudelo P, Landaeta MF, Pérez-Matus A. DNA reconciles morphology and colouration in the drunk blenny genus Scartichthys (Teleostei: Blenniidae) and provides insights into their evolutionary history. JOURNAL OF FISH BIOLOGY 2022; 100:507-518. [PMID: 34821381 DOI: 10.1111/jfb.14960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
The blenniids of the genus Scartichthys are one of the most common fishes of Central and South American Pacific coastal reefs. This being said, Scartichthys spp. remain difficult to identify in the field, and identification is particularly challenging across the c. 6000 km where three of the four currently accepted species are known to occur in sympatry. A reason for this is that the main taxonomic characters from traditional taxonomy are indeed elusive. In addition, at the same time, species can display multiple colour patterns in the field, depending on their ontogenetic stage, habitat association and reproductive behaviour. Overall, molecular characterization is warranted to help address these issues. In this study, the authors have used a novel approach to revise the genus by combining colouration, morphological and molecular data of representative specimens of the four currently valid species and seven described colour patterns. From this, the authors show that only three of the four species should be considered as valid; Scartichthys gigas (Steindachner, 1876), Scartichthys variolatus (Valenciennes, 1836) and Scartichthys viridis (Valenciennes, 1836), whereas Scartichthys crapulatus (Williams, 1990) should be synonymized with S. viridis. In the same way, the analyses in this study show that one of the colour patterns attributed so far only to S. gigas is characteristic of the juvenile stages of S. viridis. The time-calibrated phylogeny of this study shows that this genus is relatively young and that the estimated time of divergence between S. gigas and S. viridis is c. 1.71 Ma. In comparison, the Desventuradas and Juan Fernandez Islands endemic S. variolatus diverged c. 1.95 Ma. The results of this study help to clarify the taxonomy of Scartichthys.
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Affiliation(s)
- Erwan Delrieu-Trottin
- ISEM, CNRS, EPHE, IRD, Université de Montpellier, Montpellier cedex 5, France
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Hans Hartmann-Salvo
- Subtidal Ecology Laboratory, Estación Costera de Investigaciones Marinas, Departamento de Ecología, Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas (ICAEV), Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
| | - Mauricio F Landaeta
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
- Laboratorio de Ictioplancton (LABITI), Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Observación Marino para Estudios del Ambiente Costero (COSTA-R), Universidad de Valparaíso, Valparaíso, Chile
| | - Alejandro Pérez-Matus
- Subtidal Ecology Laboratory, Estación Costera de Investigaciones Marinas, Departamento de Ecología, Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
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Nelson HV, Frankham GJ, Leo V, Anson JR, Eldridge MDB, de Bruyn M. Conservation genomics of the ‘Endangered’ long-nosed bandicoot (Perameles nasuta) population at North Head, Sydney, Australia. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01356-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Santaquiteria A, Siqueira AC, Duarte-Ribeiro E, Carnevale G, White W, Pogonoski J, Baldwin CC, Ortí G, Arcila D, Betancur RR. Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences. Syst Biol 2021; 70:1145-1162. [PMID: 33892493 DOI: 10.1093/sysbio/syab028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 11/14/2022] Open
Abstract
The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.
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Affiliation(s)
- Aintzane Santaquiteria
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Alexandre C Siqueira
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Emanuell Duarte-Ribeiro
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, via Valperga Caluso 35, 10125, Torino, Italy
| | - William White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - John Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | - Guillermo Ortí
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA.,Department of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA
| | - Dahiana Arcila
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA.,Sam Noble Oklahoma Museum of Natural History, 2401 Chautauqua Ave, Norman, OK 73072, USA
| | - Ricardo R Betancur
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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Tea YK, Xu X, DiBattista JD, Lo N, Cowman PF, Ho SYW. Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus). Syst Biol 2021; 71:1-12. [PMID: 33620490 DOI: 10.1093/sysbio/syab012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 01/22/2023] Open
Abstract
The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10% of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene-Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene-Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.
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Affiliation(s)
- Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia.,Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, New South Wales 2010, Australia
| | - Xin Xu
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia.,College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, New South Wales 2010, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland 4810, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia
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Evolutionary origin of the Atlantic Cabo Verde nibbler (Girella stuebeli), a member of a primarily Pacific Ocean family of antitropical herbivorous reef fishes. Mol Phylogenet Evol 2020; 156:107021. [PMID: 33248204 DOI: 10.1016/j.ympev.2020.107021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/21/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022]
Abstract
Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli and the remaining nibbler taxa. Based on thousands of genomic markers (RAD sequences), we identified the closest relatives of G. stuebeli as being a clade of three species endemic to the northwestern Pacific, restricted to the Sea of Japan and vicinity. This clade diverged from G. stuebeli approximately 2.2 Mya. Two alternative potential routes of migration may explain this affinity: a western route, from the Tropical Eastern Pacific and the Tropical Western Atlantic, and an eastern route via the Indian Ocean and Southern Africa. The geological history and oceanography of the regions combined with molecular data presented here, suggest that the eastern route of invasion (via the Indian Ocean and Southern Africa) is a more likely scenario.
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Tea YK, Gill AC, Senou H. Two New Species of Pseudojuloides from Western Australia and Southern Japan, with a Redescription of Pseudojuloides elongatus (Teleostei: Labridae). COPEIA 2020. [DOI: 10.1643/ci-19-316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia; (YKT) . Send reprint requests to YKT
| | - Anthony C. Gill
- Ichthyology, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia
| | - Hiroshi Senou
- Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Odawara, Kanagawa 250-0031, Japan;
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van Deventer R, Rhode C, Marx M, Roodt-Wilding R. The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform. Genomics 2020; 112:3455-3464. [PMID: 32574831 DOI: 10.1016/j.ygeno.2020.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 04/17/2020] [Indexed: 12/30/2022]
Abstract
Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide polymorphism (SNP) markers for blue wildebeest. The DArTseq genotyping platform, commonly used in polyploid plant species, was selected for SNP discovery. A limited number of published articles have described the use of the DArTseq platform in animals and, therefore, this study also provided a unique opportunity to assess the performance of the DArTseq platform in an animal species. A total of 20,563 SNPs, each located within a 69 bp sequence, were generated. The developed SNP markers had a high average scoring reproducibility (>99%) and a low percentage missing data (~9.21%) compared to other reduced representation sequencing approaches that have been used in animal studies. Furthermore, the number of candidate SNPs per nucleotide position decreased towards the 3' end of sequence reads, and the ratio of transitions (Ts) to transversions (Tv) remained similar for each read position. These observations indicate that there was no read position bias, such as the identification of false SNPs due to low sequencing quality, towards the tail-end of sequencing reads. The DArTseq platform was also successful in identifying a large number of informative SNPs with desirable polymorphism parameters such as a high minor allele frequency (MAF). The Bos taurus genome was used for the in silico mapping of the marker sequences and a total of 6020 (29.28%) sequences were successfully mapped against the bovine genome. The marker sequences mapped to all of the bovine chromosomes establishing the genome-wide distribution of the SNPs. Moreover, the high observed Ts:Tv ratio (2.84:1) indicate that the DArTseq platform targeted gene-rich regions of the blue wildebeest genome. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions indicating that these SNP markers can be useful in functional gene studies. The DArTseq platform, therefore, represents a high-throughput, robust and cost-effective genotyping platform, which may find adoption in several other African antelope and animal species.
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Affiliation(s)
- Riana van Deventer
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa; Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
| | - Munro Marx
- Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
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